def test__resolve_config_dict():
input_dict = {
"network": "./circuit_config.json",
"simulation": "./simulation_config.json"
}
with pytest.raises(BluepySnapError):
test_module.Simulation(input_dict)
input_dict = {
"network": str(TEST_DATA_DIR / "./circuit_config.json"),
"simulation": str(TEST_DATA_DIR / "./simulation_config.json")
}
simulation = test_module.Simulation(input_dict)
assert simulation.config["network"] == str(TEST_DATA_DIR /
'circuit_config.json')
assert set(simulation.circuit.nodes) == {'default', 'default2'}
input_dict = json.load(
open(str(TEST_DATA_DIR / "./simulation_config.json"), "r"))
with pytest.raises(BluepySnapError):
test_module.Simulation(input_dict)
input_dict['mechanisms_dir'] = "/abspath"
input_dict["manifest"]["$OUTPUT_DIR"] = str(TEST_DATA_DIR / "reporting")
input_dict["manifest"]["$INPUT_DIR"] = str(TEST_DATA_DIR)
simulation = test_module.Simulation(input_dict)
assert simulation.config["network"] == str(TEST_DATA_DIR /
'circuit_config.json')
assert set(simulation.circuit.nodes) == {'default', 'default2'}
def test__resolve_config():
simulation = test_module.Simulation(str(TEST_DATA_DIR / 'config.json'))
assert simulation.config["network"] == str(TEST_DATA_DIR /
'circuit_config.json')
assert set(simulation.circuit.nodes) == {'default', 'default2'}
simulation = test_module.Simulation(
str(TEST_DATA_DIR / 'config_sim_no_network.json'))
assert simulation.config["network"] == str(TEST_DATA_DIR /
'circuit_config.json')
assert set(simulation.circuit.nodes) == {'default', 'default2'}
def test__resolve_config():
simulation = test_module.Simulation(str(TEST_DATA_DIR / "config.json"))
assert simulation.config["network"] == str(TEST_DATA_DIR /
"circuit_config.json")
assert set(simulation.circuit.nodes) == {"default", "default2"}
simulation = test_module.Simulation(
str(TEST_DATA_DIR / "config_sim_no_network.json"))
assert simulation.config["network"] == str(TEST_DATA_DIR /
"circuit_config.json")
assert set(simulation.circuit.nodes) == {"default", "default2"}
def test_unknown_report():
simulation = test_module.Simulation(
str(TEST_DATA_DIR / 'simulation_config.json'))
simulation.config["reports"] = {
"soma_report": {
"cells": "Layer23",
"variable_name": "m",
"sections": "unknown"
}
}
with pytest.raises(BluepySnapError):
simulation.reports
def test_all():
simulation = test_module.Simulation(
str(TEST_DATA_DIR / 'simulation_config.json'))
assert simulation.config["network"] == str(TEST_DATA_DIR /
'circuit_config.json')
assert sorted(list(simulation.circuit.nodes)) == ['default', 'default2']
assert list(simulation.circuit.edges) == ['default']
assert simulation.run == {
"tstop": 1000.0,
"dt": 0.01,
"spike_threshold": -15,
"nsteps_block": 10000,
"seed": 42
}
assert simulation.time_start == 0.
assert simulation.time_stop == 1000.
assert simulation.dt == 0.01
assert simulation.time_units == "ms"
assert simulation.simulator == "my_simulator"
assert simulation.conditions == {
"celsius": 34.0,
"v_init": -80,
"other": "something"
}
assert simulation.node_sets.resolved == {"Layer23": {"layer": [2, 3]}}
assert isinstance(simulation.spikes, SpikeReport)
assert isinstance(simulation.spikes["default"], PopulationSpikeReport)
assert sorted(list(simulation.reports)) == sorted(
list(['soma_report', 'section_report']))
assert isinstance(simulation.reports['soma_report'], SomaReport)
assert isinstance(simulation.reports['section_report'], CompartmentReport)
rep = simulation.reports['soma_report']
assert sorted(list(rep.population_names)) == ["default", "default2"]
assert isinstance(rep['default'], PopulationSomaReport)
rep = simulation.reports['section_report']
assert sorted(list(rep.population_names)) == ["default", "default2"]
assert isinstance(rep['default'], PopulationCompartmentReport)
def test_no_node_set():
simulation = test_module.Simulation(
str(TEST_DATA_DIR / 'simulation_config.json'))
# replace the _config dict with random one that does not contain "node_sets_file" key
simulation._config = {"key": "value"}
assert simulation.node_sets == {}
def test_no_network_config():
simulation = test_module.Simulation(
str(TEST_DATA_DIR / 'simulation_config_no_network.json'))
with pytest.raises(BluepySnapError):
simulation.circuit